Computing Inside a Living Cell

First time accepted submitter Rozanne writes "The new issue of Stanford Medicine magazine has a story on Stanford professor Drew Endy's creation of microscopic computers out of biological components for use inside living cells. His work is a mash-up of molecular biology and computer engineering: Instead of a computer made of silicon, metal and plastic, it's a computer made of DNA, RNA and enzymes. Endy says biologists are typically confounded at first when he explains how the computers work and how they could be used."

Comments

Re:My feeling

[OhANameWhatName]

Based on not reading the article, is that probably there is not really an analogy with computing figured out in detail. Yet.

As a fellow uninformed member of the /. community, I'd like to second your notion and move for a vote.

All those in favor of calling Drew Endy nasty names, say "I"

Endy is no longer the leader in this field

[Anonymous Coward]

For all his talk, Drew Endy hasn't actually pushed the synthetic biology field forward, and it was always questionable whether his vision of "standardized biological parts" would be the best way to engineer biology. His analogies to computer engineering are mostly false, as biology operates according to physical and chemical rules. Not Ohm's Law. Not digital logic. You can engineer biology to mimic digital logic, but it's truly analog governed by biomolecular interactions and stochastic dynamical processes.

There are other people in the Synthetic Biology field who are doing much more innovative and interesting work.
Go read stories about them.

Re:Endy is no longer the leader in this field

[Gravis Zero]

His analogies to computer engineering are mostly false, as biology operates according to physical and chemical rules. Not Ohm's Law. Not digital logic. You can engineer biology to mimic digital logic, but it's truly analog governed by biomolecular interactions and stochastic dynamical processes.

(human) brains are both analog and digital simultaneously.

even if you argue it's really all analog, the fact that you can mentally process digital logic means that you are digital computer... with lots of extra features. :)

Re:Endy is no longer the leader in this field

[Daniel Dvorkin]

Yeah. I don't know enough about his work to comment, but when I read the part about how all this computational stuff is just too confusing for those poor biologists, my bullshit alarms went off. Speaking as a bioinformaticist, whose job it is to bridge the bio/CS gap all the time, I've observed that computer scientists often have at least as hard a time grasping biology as biologists have grasping computer science. Endy's kind of smugness does no one any good.

Mutation

[DigiShaman]

Mutation is the result of DNA change. Often from external sources such as radiation or chemicals. The change could be good, bad, or nothing readily noticeable. So that said, how can you rely on the results of a biological computer that's prone to mutation and thus corrupting the results?

Re:Mutation

[sqrt(2)]

At its lowest level, the hardware we use today to store data is prone to errors. Your HDD functions perfectly well misreading data hundreds of times a second. You don't even notice until it becomes especially bad; when the errors overwhelm the ability to check and correct the data. A certain amount of errors are expected, and correctable. The simplest method is a simple checksum. Report the intended length of the message you're sending and the receipient then checks to make sure at least the length is correct. Then you can build in redundancy and error correction through more sophisticated means. These problems have largely been solved in the abstract, so they're not dependent on any particular media.

Re:My feeling

[anubi]

If you want some more detailed explanation, I would suggest reading about what Craig Venter's take on it is. He is one of the principal researchers on the Human Genome Project, and has taken the time to write a book for the layman to grasp the magnificence of what he has found.

http://www.amazon.com/Life-Speed-Light-Double-Digital/dp/0670025402

This book was released October 17, just a few days ago...

Gambling!

[antifoidulus]

Now we can finally start betting on sperm races. All you need to do is the following:

1. Put a tiny bit of compute power in each sperm cell that identifies the sperm.

2. Proceed to give odds, take bets
3. Fuck

4. Profit! After the egg has been fertilised you can use the tracking chip in the sperm to see which one "won".

Yes, yes, very nice...

[tutufan]

but can it mine bitcoins?!

the most important part: it's free for everyone

[Gravis Zero]

With electronic signal amplification, a very small change in electrical flow is sufficient to open and close gates that control massive rivers of electrons. “The biological transistor, what we call a ‘transcriptor,’ does the same thing.

He has formally donated the transcriptor and biological logic gates to the public domain via the BioBrick Public Agreement. That means anyone is free to use them. A similar declaration for the biological Internet is in process.
The only piece of biocomputer technology Stanford and Endy have patented is the biological digital memory.
“Some other groups have patented technologies claiming to accomplish a similar goal,” explains Endy. “If we have a patent, we can assure the technology is free and available to all simply by not pursuing our patent rights. But if we don’t have a patent, someone else could claim the technology and restrict its use.”

finally someone that invents a great technology and understands that patents stifle innovation!

bold tag! :)

Re:just one question.

[Chrontius]

Bend over...